Genomes of Tiny Microbes Yield Clues to Global Climate Change

WALNUT CREEK, CA — By analyzing the genomes of several microscopic ocean-dwelling organisms sequenced at the U.S. Department of Energy’s Joint Genome Institute (JGI), scientists are gaining new insights into how the planet’s oceans affect its climate.

Prochlorococcus

Comparative studies of four types of cyanobacteria — “photosynthetic” microbes that derive energy from sunlight, just like plants — were published today on the websites of the journals Nature and Proceedings of the National Academy of Sciences (PNAS). Three of the microbes — two strains of Prochlorococcus and one of Synechococcus — were among the first organisms to have their DNA sequenced at JGI in the late 1990s, and are the first ocean bacteria to be sequenced.

Synechococcus

Cyanobacteria are important in part because of their ability to turn sunlight and carbon into organic material. As the smallest yet most abundant photosynthetic organisms in the oceans, cyanobacteria play a critical role in regulating atmospheric carbon dioxide, a chief contributor to global climate change. Scientists estimate that Prochlorococcus and Synechococcus remove about 10 billion tons of carbon from the air each year as much as two-thirds of the total carbon fixation that occurs in the oceans.

Patrick Chain, a biologist at Lawrence Livermore National Laboratory (LLNL) and co-author of the two Nature papers, said the three cyanobacteria sequenced by JGI were “hand-picked” to help scientists “begin to understand the physiological and genetic controls of photosynthesis, nitrogen fixation and carbon cycling.” The sequencing was funded by the DOE Office of Science’s Office of Biological and Environmental Research as part of its mission to study climate change and carbon management.

“While many questions remain,” said Dr. Raymond L. Orbach, director of DOE’s Office of Science, “it’s clear that Prochlorococcus and Synechococcus play an immensely significant role in photosynthetic ocean carbon sequestration. Having the completed genome in hand gives us a first albeit crude ‘parts list’ to use in exploring the mechanisms for these and other important processes that could be directly relevant to this critical DOE mission.”

Along with their contribution to the global carbon cycle, the cyanobacteria are of interest to scientists because of their ability to turn sunlight into chemical energy a potential model for sustainable energy production. Before their DNA was decoded and analyzed, however, little was known about the molecular machinery these single-celled organisms use to perform their alchemy.

“It behooves us to understand exactly how, with roughly 2,000 genes, this tiny cell converts solar energy into living biomass basic elements, into life,” said Sallie W. (Penny) Chisholm, Professor of Environmental Studies at the Massachusetts Institute of Technology.

“These cells are not just some esoteric little creatures,” she continued. “They dominate the oceans. There are some 100 million Prochlorococcus cells per liter of seawater, for example.” Chisholm, a coauthor of one of the Nature papers, was part of the team that first described Prochlorococcus in 1988.

In one of the Nature papers, a team led by Gabrielle Rocap, assistant professor of oceanography at the University of Washington, reports on and compares the DNA sequence of two Prochlorococcus strains. In the other, a team led by Brian Palenik of the Scripps Institution of Oceanography at the University of California, San Diego, describes the Synechococcus genome. The PNAS paper, written by a team led by Frederick Partensky of the Roscoff Biological Station in Brittany, France, reports on the genome of a third strain of Prochlorococcus.

The two Prochlorococcus and the Synechococcus genomes sequenced by JGI were analyzed by the Genome Analysis Group of the Life Sciences Division at DOE’s Oak Ridge National Laboratory. ORNL’s Frank W. Larimer said a comparison of the genome sequences of the three organisms shows the genetic basis for the physiological adaptation of each species to its particular ecological niche at different depths in the surface waters of the ocean.

According to the authors, the Prochlorococcus comparison reveals “dynamic genomes which are constantly changing in response to myriad selection pressures. Although the two strains have 1,350 genes in common, a significant number are not shared, which have either been differentially retained from the common ancestor, or acquired through duplication or lateral transfer. Some of these genes play obvious roles in determining the relative fitness of the (strains) in response to key environmental variables,” the authors report, “and hence in regulating their distribution and abundance in the oceans.”

LLNL’s Chain noted that the genome of one of the Prochlorococcus strains is significantly smaller than the other. “Among many other interesting findings,” he said, “the genome sequences reveal that differential gene loss has played a major role in defining the photosynthetic apparatus from which these organisms derive their energy.”

Along with the Department of Energy, the research was supported by the National Science Foundation, the Seaver Foundation, the Israel-U.S. Binational Science Foundation, and France’s FP5-Margenes.

JGI was established in 1997 by the three DOE national laboratories managed by the University of California: Lawrence Livermore and Lawrence Berkeley in California and Los Alamos in New Mexico. In addition to its microbial sequencing projects, JGI has whole-genome sequencing programs that include vertebrates, fungi, and plants.